This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MPICH primary repository". The branch, master has been updated via 006a54bd1d330d16f9491dbd59dd3e8486cf7ae2 (commit) via 5b6a4eee85eca234fcc7a3886ad17c45ac3aaf5d (commit) via 3131496aab92a8ec2bd510f82c04452f55ab72ea (commit) via 7ab2a21fa340c71e7e0cc8ca3bf8d50d710585e7 (commit) from 1cc48e34f182c08ada0ce554fce35c545d336817 (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- http://git.mpich.org/mpich.git/commitdiff/006a54bd1d330d16f9491dbd59dd3e8486... commit 006a54bd1d330d16f9491dbd59dd3e8486cf7ae2 Author: Paul Coffman <[email protected]> Date: Tue Jul 15 15:47:32 2014 -0500 BALANCECONTIG cleanups/fixes use ADIOI_Assert to guard againt infinite loop; simpler easier-to-read code for fd_size assignment Signed-off-by: Rob Latham <[email protected]> diff --git a/src/mpi/romio/adio/ad_gpfs/ad_gpfs_aggrs.c b/src/mpi/romio/adio/ad_gpfs/ad_gpfs_aggrs.c index dc2b22e..48f98b8 100644 --- a/src/mpi/romio/adio/ad_gpfs/ad_gpfs_aggrs.c +++ b/src/mpi/romio/adio/ad_gpfs/ad_gpfs_aggrs.c @@ -331,6 +331,7 @@ void ADIOI_GPFS_Calc_file_domains(ADIO_File fd, * ion as well */ for (j=0;j<naggs_large;j++) { int foundbridge = 0; + int numbridgelistpasses = 0; while (!foundbridge) { if (tmpbridgelistnum[bridgeiter] > 0) { foundbridge = 1; @@ -339,12 +340,21 @@ void ADIOI_GPFS_Calc_file_domains(ADIO_File fd, printf("naggs is %d bridgeiter is %d bridgelistoffset[bridgeiter] is %d tmpbridgelistnum[bridgeiter] is %d\n",naggs, bridgeiter,bridgelistoffset[bridgeiter],tmpbridgelistnum[bridgeiter]); printf("naggs is %d bridgeiter is %d setting fd_size[%d]\n",naggs, bridgeiter,bridgelistoffset[bridgeiter]+(fd->hints->bridgelistnum[bridgeiter]-tmpbridgelistnum[bridgeiter])); */ - fd_size[bridgelistoffset[bridgeiter]+(fd->hints->fs_hints.bg.bridgelistnum[bridgeiter]-tmpbridgelistnum[bridgeiter])] = - (nb_cn_small+1) * blksize; + int currentbridgelistnum = + (fd->hints->fs_hints.bg.bridgelistnum[bridgeiter]- + tmpbridgelistnum[bridgeiter]); + int currentfdsizeindex = bridgelistoffset[bridgeiter] + + currentbridgelistnum; + fd_size[currentfdsizeindex] = (nb_cn_small+1) * blksize; tmpbridgelistnum[bridgeiter]--; } - if (bridgeiter == (fd->hints->fs_hints.bg.numbridges-1)) + if (bridgeiter == (fd->hints->fs_hints.bg.numbridges-1)) { + /* guard against infinite loop - should only ever make 1 pass + * thru bridgelist */ + ADIOI_Assert(numbridgelistpasses == 0); + numbridgelistpasses++; bridgeiter = 0; + } else bridgeiter++; } http://git.mpich.org/mpich.git/commitdiff/5b6a4eee85eca234fcc7a3886ad17c45ac... commit 5b6a4eee85eca234fcc7a3886ad17c45ac3aaf5d Author: Paul Coffman <[email protected]> Date: Fri Jul 11 23:53:22 2014 -0500 resource cleanup in p2pcontig case P2PCONTIG memory leak fixes - MPI_Request cleanups via MPI_Wait for MPI_Isends Signed-off-by: Rob Latham <[email protected]> diff --git a/src/mpi/romio/adio/common/p2p_aggregation.c b/src/mpi/romio/adio/common/p2p_aggregation.c index 20caf8d..b8e00e8 100644 --- a/src/mpi/romio/adio/common/p2p_aggregation.c +++ b/src/mpi/romio/adio/common/p2p_aggregation.c @@ -146,6 +146,7 @@ void ADIOI_P2PContigWriteAggregation(ADIO_File fd, MPI_Request *mpiSendDataToTargetAggRequest = (MPI_Request *) ADIOI_Malloc(numTargetAggs * sizeof(MPI_Request)); MPI_Status mpiWaitAnyStatusFromTargetAggs,mpiWaitAnyStatusFromSourceProcs; + MPI_Status mpiIsendStatusForSize, mpiIsendStatusForData; // use the write buffer allocated in the file_open char *write_buf0 = fd->io_buf; @@ -176,6 +177,7 @@ void ADIOI_P2PContigWriteAggregation(ADIO_File fd, int *dataSizeGottenThisRoundPerProc = (int *)ADIOI_Malloc(numSourceProcs * sizeof(int)); int *mpiRequestMapPerProc = (int *)ADIOI_Malloc(numSourceProcs * sizeof(int)); + int *mpiSendRequestMapPerProc = (int *)ADIOI_Malloc(numTargetAggs * sizeof(int)); #ifdef ROMIO_GPFS endTimeBase = MPI_Wtime(); @@ -201,7 +203,7 @@ void ADIOI_P2PContigWriteAggregation(ADIO_File fd, } int numRecvToWaitFor = 0; - int irecv; + int irecv,isend; /* the source procs receive the amount of data the aggs want them to send */ #ifdef ROMIO_GPFS @@ -242,7 +244,9 @@ void ADIOI_P2PContigWriteAggregation(ADIO_File fd, } - // the source procs send the requested data to the aggs - only send if requested more than 0 bytes + int numDataSendToWaitFor = 0; + /* the source procs send the requested data to the aggs - only send if + * requested more than 0 bytes */ for (i = 0; i < numRecvToWaitFor; i++) { MPI_Waitany(numRecvToWaitFor,mpiSizeToSendRequest,&irecv,&mpiWaitAnyStatusFromTargetAggs); @@ -255,6 +259,8 @@ void ADIOI_P2PContigWriteAggregation(ADIO_File fd, targetAggsForMyData[irecv],0,fd->comm,&mpiSendDataToTargetAggRequest[irecv]); totalAmountDataSent += amountOfDataReqestedByTargetAgg[irecv]; bufferOffsetToSendPerTargetAgg[irecv] += amountOfDataReqestedByTargetAgg[irecv]; + mpiSendRequestMapPerProc[numDataSendToWaitFor] = irecv; + numDataSendToWaitFor++; } } @@ -308,6 +314,14 @@ void ADIOI_P2PContigWriteAggregation(ADIO_File fd, } + /* clean up the MPI_Request object for the MPI_Isend which told the + * source procs how much data to send */ + for (i=0;i<numSourceProcs;i++) { + MPI_Waitany(numSourceProcs,mpiSendDataSizeRequest, + &isend,&mpiIsendStatusForSize); + } + + #ifdef ROMIO_GPFS endTimeBase = MPI_Wtime(); gpfsmpio_prof_cw[GPFSMPIO_CIO_T_DEXCH_NET] += (endTimeBase-startTimeBase); @@ -361,6 +375,10 @@ void ADIOI_P2PContigWriteAggregation(ADIO_File fd, if (iAmUsedAgg) currentRoundFDStart += coll_bufsize; + for (i = 0; i < numDataSendToWaitFor; i++) { + MPI_Wait(&mpiSendDataToTargetAggRequest[mpiSendRequestMapPerProc[i]], + &mpiIsendStatusForData); + } } // for-loop roundIter @@ -396,6 +414,7 @@ void ADIOI_P2PContigWriteAggregation(ADIO_File fd, ADIOI_Free(mpiSendDataToTargetAggRequest); ADIOI_Free(dataSizeGottenThisRoundPerProc); ADIOI_Free(mpiRequestMapPerProc); + ADIOI_Free(mpiSendRequestMapPerProc); /* TODO: still need a barrier here? */ MPI_Barrier(fd->comm); @@ -544,7 +563,7 @@ void ADIOI_P2PContigReadAggregation(ADIO_File fd, MPI_Request *mpiSendDataSizeRequest = (MPI_Request *) ADIOI_Malloc(numTargetProcs * sizeof(MPI_Request)); MPI_Request *mpiSendDataToTargetProcRequest = (MPI_Request *) ADIOI_Malloc(numTargetProcs * sizeof(MPI_Request)); - MPI_Status mpiWaitAnyStatusFromTargetAggs,mpiWaitAnyStatusFromSourceProcs; + MPI_Status mpiWaitAnyStatusFromTargetAggs,mpiWaitAnyStatusFromSourceProcs,mpiIsendStatusForSize,mpiIsendStatusForData; /* use the two-phase buffer allocated in the file_open - no app should ever * be both reading and writing at the same time */ @@ -590,7 +609,7 @@ void ADIOI_P2PContigReadAggregation(ADIO_File fd, int roundIter; for (roundIter=0;roundIter<numberOfRounds;roundIter++) { - int irecv; + int irecv,isend; // determine what offsets define the portion of the file domain the agg is reading this round if (iAmUsedAgg) { @@ -768,6 +787,16 @@ void ADIOI_P2PContigReadAggregation(ADIO_File fd, nextRoundFDStart = currentRoundFDStart + coll_bufsize; + + // clean up the MPI_Isend MPI_Requests + for (i=0;i<numTargetProcs;i++) { + MPI_Waitany(numTargetProcs,mpiSendDataSizeRequest, + &isend,&mpiIsendStatusForSize); + if (dataSizeSentThisRoundPerProc[isend] > 0) { + MPI_Wait(&mpiSendDataToTargetProcRequest[isend],&mpiIsendStatusForData); + } + } + MPI_Barrier(fd->comm); // need to sync up the source aggs which did the isend with the target procs which did the irecvs to give the target procs time to get the data before overwriting with next round readcontig } // for-loop roundIter http://git.mpich.org/mpich.git/commitdiff/3131496aab92a8ec2bd510f82c04452f55... commit 3131496aab92a8ec2bd510f82c04452f55ab72ea Author: Paul Coffman <[email protected]> Date: Fri Jul 11 14:27:53 2014 -0500 small memory leak on Blue Gene The BGQPLATFORM bridgelist and bridgelistnum hints need to be freed in ADIOI_Close because of the way the "create on one, reopen on all" logic and the hint processing logic interact. Signed-off-by: Rob Latham <[email protected]> diff --git a/src/mpi/romio/adio/common/ad_close.c b/src/mpi/romio/adio/common/ad_close.c index 62e18f9..c34ffa3 100644 --- a/src/mpi/romio/adio/common/ad_close.c +++ b/src/mpi/romio/adio/common/ad_close.c @@ -64,6 +64,20 @@ void ADIO_Close(ADIO_File fd, int *error_code) if (fd->hints && fd->hints->ranklist) ADIOI_Free(fd->hints->ranklist); if (fd->hints && fd->hints->cb_config_list) ADIOI_Free(fd->hints->cb_config_list); + /* This BlueGene platform-specific free must be done in the common code + * because the malloc's for these hint data structures are done at the + * scope of ADIO_Open within the SetInfo call (ADIOI_GPFS_SetInfo which + * calls ADIOI_BG_gen_agg_ranklist). They cannot be done in the + * ADIOI_GPFS_Close because of the file creation case where the + * ADIOI_GPFS_Close and re-open via ADIOI_GPFS_Open are done which results + * in a double-free - ADIOI_GPFS_Open does not redo the SetInfo... */ +#ifdef BGQPLATFORM + if (fd->hints && fd->hints->fs_hints.bg.bridgelist) + ADIOI_Free(fd->hints->fs_hints.bg.bridgelist); + if (fd->hints && fd->hints->fs_hints.bg.bridgelistnum) + ADIOI_Free(fd->hints->fs_hints.bg.bridgelistnum); +#endif + /* Persistent File Realms */ if (fd->hints->cb_pfr == ADIOI_HINT_ENABLE) { /* AAR, FSIZE, and User provided uniform File realms */ http://git.mpich.org/mpich.git/commitdiff/7ab2a21fa340c71e7e0cc8ca3bf8d50d71... commit 7ab2a21fa340c71e7e0cc8ca3bf8d50d710585e7 Author: Paul Coffman <[email protected]> Date: Mon Jul 7 20:27:30 2014 -0500 clean up resources if P2PContig selected After a call to ADIOI_P2PContig(Write/Read)Aggregation, code exits early from ADIOI_GPFS_(Write/Read)StridedColl and was not freeing some data structures Signed-off-by: Rob Latham <[email protected]> diff --git a/src/mpi/romio/adio/ad_gpfs/ad_gpfs_rdcoll.c b/src/mpi/romio/adio/ad_gpfs/ad_gpfs_rdcoll.c index 938a133..71ddb9a 100644 --- a/src/mpi/romio/adio/ad_gpfs/ad_gpfs_rdcoll.c +++ b/src/mpi/romio/adio/ad_gpfs/ad_gpfs_rdcoll.c @@ -292,6 +292,14 @@ void ADIOI_GPFS_ReadStridedColl(ADIO_File fd, void *buf, int count, /* NOTE: we are skipping the rest of two-phase in this path */ GPFSMPIO_T_CIO_REPORT( 0, fd, myrank, nprocs) + + ADIOI_Free(offset_list); + ADIOI_Free(len_list); + ADIOI_Free(st_offsets); + ADIOI_Free(end_offsets); + ADIOI_Free(fd_start); + ADIOI_Free(fd_end); + return; } } diff --git a/src/mpi/romio/adio/ad_gpfs/ad_gpfs_wrcoll.c b/src/mpi/romio/adio/ad_gpfs/ad_gpfs_wrcoll.c index eef476d..436d01d 100644 --- a/src/mpi/romio/adio/ad_gpfs/ad_gpfs_wrcoll.c +++ b/src/mpi/romio/adio/ad_gpfs/ad_gpfs_wrcoll.c @@ -278,6 +278,14 @@ void ADIOI_GPFS_WriteStridedColl(ADIO_File fd, const void *buf, int count, error_code, st_offsets, end_offsets, fd_start, fd_end); /* NOTE: we are skipping the rest of two-phase in this path */ GPFSMPIO_T_CIO_REPORT( 1, fd, myrank, nprocs) + + ADIOI_Free(offset_list); + ADIOI_Free(len_list); + ADIOI_Free(st_offsets); + ADIOI_Free(end_offsets); + ADIOI_Free(fd_start); + ADIOI_Free(fd_end); + return; } } ----------------------------------------------------------------------- Summary of changes: src/mpi/romio/adio/ad_gpfs/ad_gpfs_aggrs.c | 16 +++++++++-- src/mpi/romio/adio/ad_gpfs/ad_gpfs_rdcoll.c | 8 ++++++ src/mpi/romio/adio/ad_gpfs/ad_gpfs_wrcoll.c | 8 ++++++ src/mpi/romio/adio/common/ad_close.c | 14 ++++++++++ src/mpi/romio/adio/common/p2p_aggregation.c | 37 ++++++++++++++++++++++++--- 5 files changed, 76 insertions(+), 7 deletions(-) hooks/post-receive -- MPICH primary repository